rs2964798

chr5-10788721-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.841 in 152,258 control chromosomes in the GnomAD database, including 54,845 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.84 (54845 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.841 AC: 128006 AN: 152140 Hom.: 54812 Cov.: 34

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.851

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.841 AC: 128101 AN: 152258 Hom.: 54845 Cov.: 34 AF XY: 0.833 AC XY: 62054 AN XY: 74450

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.851

Alfa AF: 0.891 Hom.: 92606

Bravo AF: 0.838

Asia WGS AF: 0.585 AC: 2035 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2964798; hg19: chr5-10788833;